To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")

In most cases, you don't need to download the package archive at all.

phyloseq

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see phyloseq.

Handling and analysis of high-throughput microbiome census data.

Bioconductor version: 3.1

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Author: Paul J. McMurdie <mcmurdie at alumni.stanford.edu>, Susan Holmes <susan at stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie <mcmurdie at alumni.stanford.edu>

Citation (from within R, enter citation("phyloseq")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("phyloseq")

HTML R Script phyloseq analysis vignette

HTML R Script phyloseq and DESeq2 on Colorectal Cancer Data

HTML R Script phyloseq basics vignette

PDF Reference Manual

Text NEWS

Details

biocViews Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software

Version 1.12.2

In Bioconductor since BioC 2.10 (R-2.15) (4 years)

License AGPL-3

Depends R (>= 3.1.0)

Imports BiocGenerics(>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.4), DESeq2(>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10)

LinkingTo

Suggests genefilter(>= 1.42.0), testthat (>= 0.8), knitr (>= 1.3)

SystemRequirements

Enhances doParallel (>= 1.0.1)

URL http://dx.plos.org/10.1371/journal.pone.0061217

BugReports https://github.com/joey711/phyloseq/issues

Depends On Me

Imports Me

Suggests Me

Build Report